There could be a possibility that the interface between FX3 and the K-series board be noisy. FX3 has a mechanism to automatically disconnect the USB, if it is prone to more noise beyond a particular threshold.
Can you please make sure that the schematics and layout recommendations have followed in the board design? Do the GPIF lines have the 22 Ohm series termination resistors on them? Please create a Tech Support case with us for more investigation.
- Madhu Sudhan